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At least 721 records · Page 40Linked to original sources

USGS2022

Genetic diversity and connectivity of chemosynthetic cold seep mussels from the U.S. Atlantic margin

Background Deep-sea mussels in the subfamily Bathymodiolinae have unique adaptations to colonize hydrothermal-vent and cold-seep environments throughout the world ocean. These invertebrates function as important ecosystem engineers, creating heterogeneous habitat and promoting biodiversity in the deep sea. Despite their ecological significance, efforts to assess the diversity and connectivity of this group are extremely limited. Here, we present the first genomic-scale diversity assessments of the recently discovered bathymodioline cold-seep communities along the U.S. Atlantic margin, dominated by Gigantidas childressi and Bathymodiolus heckerae . Results A Restriction-site Associated DNA Sequencing (RADSeq) approach was used on 177 bathymodiolines to examine genetic diversity and population structure within and between seep sites. Assessments of genetic differentiation using single-nucleotide polymorphism (SNP) data revealed high gene flow among sites, with the shallower and more northern sites serving as source populations for deeper occurring G. childressi . No evidence was found for genetic diversification across depth in G. childressi , likely due to their high dispersal capabilities. Kinship analyses indicated a high degree of relatedness among individuals, and at least 10–20% of local recruits within a particular site. We also discovered candidate adaptive loci in G. childressi and B. heckerae that suggest differences in developmental processes and depth-related and metabolic adaptations to chemosynthetic environments. Conclusions These results highlight putative source communities for an important ecosystem engineer in the deep sea that may be considered in future conservation efforts. Our results also provide clues into species-specific adaptations that enable survival and potential speciation within chemosynthetic ecosystems.

Atlantic Ocean, Baltimore Canyon Seep, Blake Ridge↗

USGS2016

Genetic structure of faucet snail, Bithynia tentaculata populations in North Americal based on microsattelite markers

Bithynia tentaculata is believed to have been extirpated from North America during the last glacial maximum. It was reintroduced into North America via the Great Lakes basin in the 1800’s and has recently been expanding its geographic range. This snail serves as intermediate host for three trematodes that cause extensive recurring morbidity and mortality events in migratory water birds along the Mississippi River. Using twelve microsatellite loci for ~200 individual snails from 11 populations in North America and Europe, we examined one of the three major geographic regions from which founding populations into the Great Lakes typically originate. Our data supports a single recolonization of North America into the Great Lakes Basin followed by subsequent introduction events from the Great Lakes to other large watersheds in North America. However, additional watersheds in Europe require sampling to confirm this result. No populations with genetic signatures indicative of North American glacial relics were found. The initial invasion of North America was likely not from the Ponto-Caspian basin, the usual source of freshwater invasive species to the Laurentian Great Lakes.

Freshwater Mollusk Biology and Conservation↗

USGS2021

Comparative genomics analyses support the reclassification of Bisgaard taxon 40 as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as type species: Novel insights into the phylogeny and virulence factors of a Pasteurellaceae family member associated with mortality events in seabirds

The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA , ompH ) and colonization ( exbD , fur , galU , galE , lpxA , lpxC , and kdsA ) of the host and a cytolethal distending toxin ( cdt ), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201 T (=DSM 112696).

Frontiers in Microbiology↗

USGS2025

Stock composition of cryptic Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Restigouche River and estuary, Canada

The Atlantic sturgeon ( Acipenser oxyrinchus oxyrinchus ) is an important species in eastern North America due to its conservation status and cultural significance. Local Mi'gmaw fishers have reported an increase in sturgeon sightings over the last decade in the Restigouche River and estuary. Mi’gmaw Knowledge, oral history, and archaeological finds attest to their historical presence in the region; however, the river is not a documented habitat for Atlantic sturgeon in Western literature. Based on community interest and concern, the Gespe’gewa’gi Institute of Natural Understanding co-developed a Two-Eyed Seeing collaboration to learn more about these sturgeon. Here, we investigate their genetic origin via microsatellite analyses and hypothesized that they would originate from the closest spawning habitat, the St. Lawrence River. We found that, overall, the largest contributor to our Atlantic sturgeon sampled from the Restigouche River system was the St. Lawrence River (85.7% of samples), followed by the Wolastoq (3.6%), then a mixture of the St. Lawrence, the Wolastoq, the Kennebec, and/or the Hudson River populations (10.7%). Improving our understanding of the distribution of Atlantic sturgeon through microsatellite analyses and leveraging range-wide genetic baselines directly assesses the genetic origin of unknown stock compositions and can support the future co-management of the species.

Restigouche River and estuary↗

USGS2008

Hydrocarbon Source Rocks in the Deep River and Dan River Triassic Basins, North Carolina

This report presents an interpretation of the hydrocarbon source rock potential of the Triassic sedimentary rocks of the Deep River and Dan River basins, North Carolina, based on previously unpublished organic geochemistry data. The organic geochemical data, 87 samples from 28 drill holes, are from the Sanford sub-basin (Cumnock Formation) of the Deep River basin, and from the Dan River basin (Cow Branch Formation). The available organic geochemical data are biased, however, because many of the samples collected for analyses by industry were from drill holes that contained intrusive diabase dikes, sills, and sheets of early Mesozoic age. These intrusive rocks heated and metamorphosed the surrounding sediments and organic matter in the black shale and coal bed source rocks and, thus, masked the source rock potential that they would have had in an unaltered state. In places, heat from the intrusives generated over-mature vitrinite reflectance (%Ro) profiles and metamorphosed the coals to semi-anthracite, anthracite, and coke. The maximum burial depth of these coal beds is unknown, and depth of burial may also have contributed to elevated thermal maturation profiles. The organic geochemistry data show that potential source rocks exist in the Sanford sub-basin and Dan River basin and that the sediments are gas prone rather than oil prone, although both types of hydrocarbons were generated. Total organic carbon (TOC) data for 56 of the samples are greater than the conservative 1.4% TOC threshold necessary for hydrocarbon expulsion. Both the Cow Branch Formation (Dan River basin) and the Cumnock Formation (Deep River basin, Sanford sub-basin) contain potential source rocks for oil, but they are more likely to have yielded natural gas. The organic material in these formations was derived primarily from terrestrial Type III woody (coaly) material and secondarily from lacustrine Type I (algal) material. Both the thermal alteration index (TAI) and vitrinite reflectance data (%Ro) indicate levels of thermal maturity suitable for generation of hydrocarbons. The genetic potential of the source rocks in these Triassic basins is moderate to high and many source rock sections have at least some potential for hydrocarbon generation. Some data for the Cumnock Formation indicate a considerably higher source rock potential than the basin average, with S1 + S2 data in the mid-20 mg HC/g sample range, and some hydrocarbons have been generated. This implies that the genetic potential for all of these strata may have been higher prior to the igneous activity. However, the intergranular porosity and permeability of the Triassic strata are low, which makes fractured reservoirs more attractive as drilling targets. In some places, gravity and magnetic surveys that are used to locate buried intrusive rock may identify local thermal sources that have facilitated gas generation. Alternatively, awareness of the distribution of large intrusive igneous bodies at depth may direct exploration into other areas, where thermal maturation is less than the limits of hydrocarbon destruction. Areas prospective for natural gas also contain large surficial clay resources and any gas discovered could be used as fuel for local industries that produce clay products (principally brick), as well as fuel for other local industries.

North Carolina↗

USGS2021

Morphometric sex identification of nestling and free-flying Tasmanian Wedge-tailed Eagles (Aquila audax fleayi)

The endangered Tasmanian Wedge-tailed Eagle ( Aquila audax fleayi ) is the focus of continued research and conservation efforts. A tool for accurate and efficient identification of the sex of individuals would be a valuable aid to research and management. However, plumages are monomorphic between the sexes, making sex identification difficult without molecular analyses. Our aim was to assess whether Tasmanian Wedge-tailed Eagles of different age classes could be sexed accurately using morphological measurements. We took measurements of 25 live late-stage eagle nestlings and 108 carcasses of free-flying birds found opportunistically throughout Tasmania. Sex of all individuals was confirmed via genetic analyses. Free-flying birds were larger than nestlings; thus, we used age-specific statistical tools to distinguish the sexes. For both nestlings and free-flying birds, females were significantly larger than males, but overlap between the sexes prevented accurate sex identification using any single measurement. We used stepwise linear discriminant function analyses to select morphometric measurements necessary for accurate sex identification. Free-flying birds could be sexed with 97.6% accuracy using a combination of measurements of the forearm length, tarsus width (i.e., lateromedial width), and hallux length. Late-stage nestlings (9–10 wk old) could be sexed with 95.4% accuracy using measurements of the hallux width (i.e., lateromedial width), hallux breadth (i.e., anteroposterior width of hallux), and tarsus breadth (i.e., anteroposterior width of the tarsometatarsus at the narrowest point). The discriminate functions we present also allow the identification of sex in cases where morphological sex identification may be in doubt and molecular analyses should be prioritized. These equations provide a valuable research tool for studies of sexual differences in behavior and causes of mortality of this endangered subspecies.

Tasmania↗

USGS2025

Assessing diet and genotyping success of goat pellet surveys from 2019 in Glacier National Park

Fecal pellets contain genetic information and can be used to identify individuals, their diet, and more. Individual identification can be useful in understanding movements of individuals, developing population estimates, assessing vital rates, genetic diversity and structure, and evaluating trends over time (e.g., Epps et al 2024). Successful genotyping depends on the quality of the sample, which can be influenced by many things including the initial state of the sample, environmental conditions that the pellets were exposed to, and the method of storage. The diet of mountain goats ( Oreamnos americanus ) is hard to study as they are habitat specialists in some of the most remote and rugged alpine environments (Festa-Bianchet & Côté 2012). These iconic ungulates epitomize the renowned wilderness character of Glacier National Park (GNP), yet the population has declined by 45% since 2008 likely due at least in part to changing climate (Graves et al. 2025). This is well above the International Union for the Conservation of Nature’s population decline criterion used to designate a species as vulnerable (IUCN 2012). Mountain goats are known as dietary generalists employing highly variable diets across systems, but diets have not been identified for GNP. Identifying goat diet composition in GNP can provide the information needed to determine whether this population decline could be related to climate-change induced shifts in forage phenology, diversity, productivity, and plant community structure. Other anthropogenic changes in GNP, such as increases in exotic and invasive plant species, will continue to affect plant community composition (Lesica et al. 1993). These alterations may reduce optimal forage availability and quality, which could have a deleterious effect on mountain goat survival. To examine these possibilities, we must first ask- What precisely are the mountain goats of Glacier National Park eating? DNA metabarcoding of fecal pellets provides a cutting-edge, non-invasive method for assessing herbivore diet. Previous studies of mountain goat diet have used methods such as fecal crude protein analysis (Festa-Bianchet & Côté 2012), rumen analysis (Saunders 1955), fecal microhistology (Cobb et al. 2012), and bite-for-bite feeding observations (Daily et al. 1984). Many of these studies have only been able to identify diet components to functional plant type and the methods used are biased towards less digestible diet components such as grasses (McInnis et al. 1983). Metabarcoding of fecal pellets can provide a higher taxonomic resolution than previous methods (Scasta et al. 2019, Stapleton et al. 2022) and open the field for increased participation of volunteers, also called community or citizen scientists. Here, we use mountain goat fecal pellets to conduct 1) an evaluation of which conditions might influence genotyping success and 2) a preliminary assessment of diet using metabarcoding. This pilot study allowed us to evaluate which pellets to focus on collecting, identify the best storage methods, explore approaches for analyzing metabarcoding data, examine the utility of metabarcoding for acquiring taxonomically specific diet information, and to identify genetic sequences that could not be resolved to genus or species levels using these methods. We examined the frequency of occurrence and relative diet composition of identified forbs, shrubs, graminoids, mosses, and trees in mountain goat diets.

Montana↗

USGS2020

Estimating and forecasting spatial population dynamics of apex predators using transnational genetic monitoring

The ongoing recovery of terrestrial large carnivores in North America and Europe is accompanied by intense controversy. On the one hand, reestablishment of large carnivores entails a recovery of their most important ecological role, predation. On the other hand, societies are struggling to relearn how to live with apex predators that kill livestock, compete for game species, and occasionally injure or kill people. Those responsible for managing these species and mitigating conflict often lack fundamental information due to a long-standing challenge in ecology: How do we draw robust population-level inferences for elusive animals spread over immense areas? Here we showcase the application of an effective tool for spatially explicit tracking and forecasting of wildlife population dynamics at scales that are relevant to management and conservation. We analyzed the world’s largest dataset on carnivores comprising more than 35,000 noninvasively obtained DNA samples from over 6,000 individual brown bears ( Ursus arctos ), gray wolves ( Canis lupus ), and wolverines ( Gulo gulo ). Our analyses took into account that not all individuals are detected and, even if detected, their fates are not always known. We show unequivocal quantitative evidence of large carnivore recovery in northern Europe, juxtaposed with the finding that humans are the single-most important factor driving the dynamics of these apex predators. We present maps and forecasts of the spatiotemporal dynamics of large carnivore populations, transcending national boundaries and management regimes.

Proceedings of the National Academy of Sciences of↗

USGS2026

Individual encounter data of six African carnivore species optimized for multi-species density estimation

The ability to estimate abundances of multiple wildlife species within an area is valuable for both conservation and ecological inquiry. Spatially explicit capture–recapture (SCR) methods are commonly used to obtain reliable population size estimates, particularly for low-density and individually identifiable carnivore species. However, estimating abundance within multi-species communities poses a methodological challenge as survey designs and analytical tools are primarily tailored for single target species. Here, we present a dataset of spatially referenced individual encounter histories of six carnivore species with varying space requirements (lion, Panthera leo ; leopard, Panthera pardus ; spotted hyena, Crocuta crocuta ; cheetah, Acinonyx jubatus ; serval, Leptailurus serval ; large-spotted genet, Genetta tigrina ). These data were collected in a South African game reserve using a camera trap array optimized for multi-species density estimation using SCR methods. This dataset will be a valuable resource for studying spatial processes among potentially interacting carnivores without the common pitfalls that come with by-catch data of non-target species, and will provide a much-needed case study for the further development of multi-species statistical method development.

Munywana Conservancy↗

USGS2011

Predicting phenology by integrating ecology, evolution and climate science

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life‐history events. Phenology has well‐demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species’ reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.

Global Change Biology↗

USGS2020

Calibrating environmental DNA metabarcoding to conventional surveys for measuring fish species richness

The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overcomes low detection probabilities and should consequently enhance estimates of biodiversity and its proxy, species richness. Here, we synthesize 37 studies in natural aquatic systems to compare species richness estimates for bony fish between eDNA metabarcoding and conventional methods, such as nets, visual census, and electrofishing. In freshwater systems with fewer than 100 species, we found eDNA metabarcoding detected more species than conventional methods. Using multiple genetic markers further increased species richness estimates with eDNA metabarcoding. For more diverse freshwater systems and across marine systems, eDNA metabarcoding reported similar values of species richness to conventional methods; however, more studies are needed in these environments to better evaluate relative performance. In systems with greater biodiversity, eDNA metabarcoding will require more populated reference databases, increased sampling effort, and multi-marker assays to ensure robust species richness estimates to further validate the approach. eDNA metabarcoding is reliable and provides a path for broader biodiversity assessments that can outperform conventional methods for estimating species richness.

Frontiers in Ecology and Evolution↗

USGS2008

Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction. ?? 2008 Elsevier Inc.

Molecular Phylogenetics and Evolution↗

USGS2026

Bee-ing similar: Low diversity, no population structure, and signals of adaptation in two North Dakota bumble bees

Habitat fragmentation and destruction are driving widespread declines in ecosystem function, species abundance, and genetic diversity across the globe. Among the affected taxa are bumble bees (genus Bombus ), which are essential pollinators. Bumble bee declines have been linked to anthropogenic pressures such as land-use change and climate change. To better understand how the environment is shaping bumble bee populations, we employed a landscape genetics approach to examine the genetic diversity, population structure, and potential local adaptation of two widespread species— Bombus ternarius and Bombus griseocollis —across North Dakota. From 2017–2020, 161 B. ternarius and 200 B. griseocollis bumble bees were sampled in ND across 13 and 17 sites, respectively. We found low levels of heterozygosity and inbreeding across all populations for both species, with no evidence of population structure or isolation by distance. Our results revealed signatures of potential local adaptation to climatic variables and land cover characteristics, suggesting that our species are adapted to environmental gradients across the state. Having similar results between both species across all analyses suggests that other wide-ranging bumble bees in the region may share these patterns. High connectivity can buffer short-term population losses, but low genetic diversity may constrain adaptive potential and reduce resilience to future environmental change and emerging threats. Our findings have broad applicability to other pollinators and taxa facing similar environmental pressures. Both species have populations that continually exchange genes creating widespread connectivity but are still locally shaped by adaptation.

North Dakota↗

USGS1998

Genetic differentiation between wintering populations of lesser snow geese nesting on Wrangel Island, Russia

Arctic breeding populations of Lesser Snow Geese ( Chen c. caerulescens ) range from Baffin Island in eastern Canada to Wrangel Island, Russia, which is located 650 km west of Alaska (Bellrose 1980). Although hundreds of thousands of Lesser Snow Geese may have occupied the Russian arctic in the mid1800s (see Takekawa et al., 1994), the Wrangel Island birds constitute the only remnant colony on the Asian continent (Syroechkovsky and Litvin 1986) and may represent a matriarchal population for the species (Quinn 1992). In the past 30 years, the Wrangel Island colony has declined from more than 200,000 to less than 75,000 breeding adults (Pacific Flyway Technical Subcommittee 1992, V. Baranyuk unpubl. data), which has resulted in increasing concern about its conservation and management. The Wrangel Island colony consists of two wintering populations that migrate to different regions and are faithful to their wintering areas (McKelvey et al. 1989). The larger northern population (about 60% of the total from Wrangel) migrates to the Fraser River delta of British Columbia and the Skagit River delta of northern Washington, whereas the southern population flies 600 km farther south to the Central Valley of California (Rienecker 1965, Teplov and Shev. aryova 1965, Jeffrey and Kaiser 1979, Priklonsky and Sapetin 1979). The northern population is isolated from other Lesser Snow Geese during the winter, but the southern population mixes with geese from Banks Island, Canada and from the smaller Anderson and Sagaviriniktok River deltas (Dzubin 1974, Johnson 1995, Syroechkovsky et al. 1994).

The Auk↗

USGS2017

Rare-earth elements

The rare-earth elements (REEs) are 15 elements that range in atomic number from 57 (lanthanum) to 71 (lutetium); they are commonly referred to as the “lanthanides.” Yttrium (atomic number 39) is also commonly regarded as an REE because it shares chemical and physical similarities and has affinities with the lanthanides. Although REEs are not rare in terms of average crustal abundance, the concentrated deposits of REEs are limited in number. Because of their unusual physical and chemical properties, the REEs have diverse defense, energy, industrial, and military technology applications. The glass industry is the leading consumer of REE raw materials, which are used for glass polishing and as additives that provide color and special optical properties to the glass. Lanthanum-based catalysts are used in petroleum refining, and cerium-based catalysts are used in automotive catalytic converters. The use of REEs in magnets is a rapidly increasing application. Neodymium-iron-boron magnets, which are the strongest known type of magnets, are used when space and weight are restrictions. Nickel-metal hydride batteries use anodes made of a lanthanum-based alloys. China, which has led the world production of REEs for decades, accounted for more than 90 percent of global production and supply, on average, during the past decade. Citing a need to retain its limited REE resources to meet domestic requirements as well as concerns about the environmental effects of mining, China began placing restrictions on the supply of REEs in 2010 through the imposition of quotas, licenses, and taxes. As a result, the global rare-earth industry has increased its stockpiling of REEs; explored for deposits outside of China; and promoted new efforts to conserve, recycle, and substitute for REEs. New mine production began at Mount Weld in Western Australia, and numerous other exploration and development projects noted in this chapter are ongoing throughout the world. The REE-bearing minerals are diverse and often complex in composition. At least 245 individual REE-bearing minerals are recognized; they are mainly carbonates, fluorocarbonates, and hydroxylcarbonates (n = 42); oxides (n = 59); silicates (n = 85); and phosphates (n = 26). Many of the world’s significant REE deposits occur in carbonatites, which are carbonate igneous rocks. The REEs also have a strong genetic association with alkaline magmatism. The systematic geologic and chemical processes that explain these observations are not well understood. Economic or potentially economic REE deposits have been found in (a) carbonatites, (b) peralkaline igneous systems, (c) magmatic magnetite-hematite bodies, (d) iron oxide-copper-gold (IOCG) deposits, (e) xenotime-monazite accumulations in mafic gneiss, (f) ion-absorption clay deposits, and (g) monazite-xenotime-bearing placer deposits. Carbonatites have been the world’s main source for the light REEs since the 1960s. Ion-adsorption clay deposits in southern China are the world’s primary source of the heavy REEs. Monazite-bearing placer deposits were important sources of REEs before the mid-1960s and may be again in the future. In recent years, REEs have been produced from large carbonatite bodies mined at the Mountain Pass deposit in California and, in China, at the Bayan Obo deposit in Nei Mongol Autonomous Region, the Maoniuping deposit in Sichuan Province, the Daluxiang deposit in Sichuan Province, and the Weishan deposit in Anhui Province. Alkaline igneous complexes have recently been targeted for exploration because of their enrichments in the heavy REEs. Information relevant to the environmental aspects of REE mining is limited. Little is known about the aquatic toxicity of REEs. The United States lacks drinking water standards for REEs. The concentrations of REEs in environmental media are influenced by their low abundances in crustal rocks and their limited solubility in most groundwaters and surface waters. The scarcity of sulfide minerals, including pyrite, minimizes or eliminates concerns about acid-mine drainage for carbonatite-hosted deposits and alkaline-intrusion-related REE deposits. For now, insights into environmental responses of REE mine wastes must rely on predictive models.

Professional Paper↗

USGS2023

Serum virome of southern Beaufort Sea polar bears (Ursus maritimus) during a period of rapid climate change

Climate change affects the behavior, physiology and life history of many Arctic wildlife species. It can also influence the distribution and ecology of infectious agents. The southern Beaufort Sea (SB) subpopulation of polar bears ( Ursus maritimus ) has experienced dramatic behavioral changes due to retreating sea ice and other climate-related factors, but the effects of these changes on physiology and infection remain poorly understood. Using serum from polar bears sampled between 2004 and 2015 and metagenomic DNA sequencing, we identified 48 viruses, all of the family Anelloviridae . Anelloviruses are small, ubiquitous infectious agents with circular single-stranded DNA genomes that are not known to cause disease but, in humans, covary in diversity and load with immunological compromise. We therefore examined the usefulness of anelloviruses as biomarkers of polar bear physiological stress related to climate and habitat use. Polar bear anelloviruses sorted into two distinct clades on a phylogenetic tree, both of which also contained anelloviruses of giant pandas ( Ailuropoda melanoleuca ), another ursid. Neither anellovirus diversity nor load were associated with any demographic variables, behavioral factors or direct physiological measures. However, pairwise genetic distances between anelloviruses were positively correlated with pairwise differences in sampling date, suggesting that the polar bear “anellome”is evolving over time. These findings suggest that anelloviruses are not a sensitive indicator of polar physiological stress, but they do provide a baseline for evaluating future changes to polar bear viromes.

Alaska↗

USGS2010

Identification of a novel arsenite oxidase gene, arxA, in the haloalkaliphilic, arsenite-oxidizing bacterium alkalilimnicola ehrlichii strain MLHE-1

Although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). Two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (ArrA) and (ii) arsenite oxidase (AoxB). Both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (ArrA and AoxB) within the dimethyl sulfoxide (DMSO) reductase family of enzymes. Here we report on the genetic identification of a “new” type of arsenite oxidase that fills a phylogenetic gap between the ArrA and AoxB clades of arsenic metabolic enzymes. This “new” arsenite oxidase is referred to as ArxA and was identified in the genome sequence of the Mono Lake isolate Alkalilimnicola ehrlichii MLHE-1, a chemolithoautotroph that can couple arsenite oxidation to nitrate reduction. A genetic system was developed for MLHE-1 and used to show that arxA (gene locus ID mlg _ 0216 ) was required for chemoautotrophic arsenite oxidation. Transcription analysis also showed that mlg _ 0216 was only expressed under anaerobic conditions in the presence of arsenite. The mlg _ 0216 gene is referred to as arxA because of its greater homology to arrA relative to aoxB and previous reports that implicated Mlg_0216 (ArxA) of MLHE-1 in reversible arsenite oxidation and arsenate reduction in vitro . Our results and past observations support the position that ArxA is a distinct clade within the DMSO reductase family of proteins. These results raise further questions about the evolutionary relationships between arsenite oxidases (AoxB) and arsenate respiratory reductases (ArrA). Arsenic is toxic to most organisms and is known to cause cancer in humans. However, bacteria have adapted several biotransformation pathways that function to either couple the reduction or oxidation of arsenicals to energy conservation and growth (1). The enzymologies of these two pathways have several features in common. The arsenate respiratory reductase (ArrAB) and arsenite oxidase (AoxAB) enzymes are usually composed of at least two subunits, a small iron-sulfur cluster-containing subunit (ArrB and AoxA) and a larger molybdopterin-containing catalytic subunit (ArrA and AoxB). Although they catalyze arsenic redox chemistry, ArrA and AoxB form distinct phylogenetic clades within the dimethyl sulfoxide (DMSO) reductase family of molybdenum-containing enzymes (16, 24). Culture-dependent approaches have resulted in the isolation of a variety of diverse bacteria that metabolize arsenic (reviewed in reference 26). Many of these isolates have had their genomes sequenced, which has been insightful for understanding the composition and diversity of arr and aox gene clusters. In the arsenite-oxidizing nitrate reducer Alkalilimnicola ehrlichii strain MLHE-1 (a haloalkaliphile isolated from Mono Lake [CA]) (10, 15), bioinformatic analysis of its genome revealed the absence of genes homologous to the arsenite oxidase genes of the aoxB type. Instead, two genes ( mlg _ 0216 and mlg _ 2426 ) were identified that better resembled the catalytic subunit of the arsenate respiratory reductase (20); however, MLHE-1 has not been shown to respire (or reduce) arsenate (15). Recent work by Richey et al. (20) showed that the Mlg_0216 protein (and not Mlg_2426) was expressed under chemolithoautotrophic (10 mM arsenite and 10 mM nitrate) growth conditions. Moreover, it was shown that Mlg_0216 exhibits both arsenate reductase and arsenite oxidase activities in vitro . These observations raised the question, is the mlg _ 0216 gene required for arsenite oxidation in vivo ? In this report, we addressed this question by developing a genetic system in MLHE-1, generating strains with mutations in mlg _ 0216 and mlg _ 2426 , and physiologically characterizing the resulting strains. Our results implicate mlg _ 0216 in chemolithoautotrophic arsenite oxidation coupled to nitrate respiration.

Journal of Bacteriology↗

USGS2016

Jaguar taxonomy and genetic diversity for southern Arizona, United States, and Sonora, Mexico

Executive Summary The jaguar is the largest Neotropical felid and the only extant representative of the genus Panthera in the Americas. In recorded history, the jaguars range has extended from the Southern United States, throughout Mexico, to Central and South America, and they occupy a wide variety of habitats. A previous jaguar genetic study found high historical levels of gene flow among jaguar populations over broad areas but did not include any samples of jaguar from the States of Arizona, United States, or Sonora, Mexico. Arizona and Sonora have been part of the historical distribution of jaguars; however, poaching and habitat fragmentation have limited their distribution until they were declared extinct in the United States and endangered in Sonora. Therefore, a need was apparent to have this northernmost (Arizona/Sonora) jaguar population included in an overall jaguar molecular taxonomy and genetic diversity analyses. In this study, we used molecular genetic markers to examine diversity and taxonomy for jaguars in the Northwestern Jaguar Recovery Unit (NJRU; Sonora, Sinaloa, and Jalisco, Mexico; and southern Arizona and New Mexico, United States) relative to jaguars in other parts of the jaguar range (Central and South America). The objectives of this study were to: Collect opportunistic jaguar samples (hide, blood, hair, saliva, and scat), from historical and current individuals, that originated in NJRU areas of Arizona, New Mexico, and Sonora; Use these samples to assess molecular taxonomy of NJRU jaguars compared to data from a previous study of jaguars rangewide; and Develop suggestions for conservation of NJRU jaguars based on the results.

Arizona, Jalisco, New Mexico, Sonora, Sinaloa↗